A woman who mentored students in a Manhattan after-school program was arrested Thursday for having inappropriate sexual conduct with a student, authorities said.

For months, Aylin Canon, 29, engaged in sexual conduct with a 13-year-old girl last year in “multiple locations” including Canon’s Manhattan apartment and at Public School 188, The Island School on the Lower East Side, according to the special commissioner of investigation for city schools.

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Canon was charged with three counts each of criminal sex acts, sex abuse and endangering the welfare of a child. She worked with Education Alliance, a community-based organization that provided after-school programs.

She was fired in May.

“There is no place in the New York City school system for those who prey on children,” said the special commissioner, Anastasia Coleman.

Prosecutors alleged the relationship lasted for four months.

Canon’s mom, who didn’t give her name, claimed the teen victim lied about her age.

“It’s a lie. It was a setup. The girl said she was 17, not 13,” said the mom, who wept as she watched her daughter’s arraignment in Manhattan Criminal Court.

“My daughter is a good girl,” Canon’s mom said. “She’s never had a criminal record. She has a good job in a good school. She wouldn’t do anything like this.”

A judge ordered Canon held on $35,000 bail.

An Education Department spokesman, Doug Cohen, said Canon is barred from working in city schools.

“These are deeply disturbing allegations … She was never a DOE employee and will not work in a New York City public school again,” Cohen said.